More on this; it seems that the problem is caused by the following:
'Convert book' (input RTF -> output EPUB)
Within the 'Convert' dialog, go to 'Page Setup'
Note that the default Output Profile on this page is still set to 'Kindle'. When this is changed to 'Default output profile', then the problem goes away.

I think there's still an issue insofar as the output profile should follow what was selected at the initial stage, not default to something that may no longer make any sense in the context. Subtle, though...